mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
231 lines
6.5 KiB
OpenEdge ABL
231 lines
6.5 KiB
OpenEdge ABL
/*
|
|
* $Id$
|
|
*
|
|
* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
|
|
* All rights reserved.
|
|
*
|
|
* Redistribution and use in source and binary forms, with or without
|
|
* modification, are permitted provided that the following conditions are
|
|
* met:
|
|
*
|
|
* * Redistributions of source code must retain the above copyright
|
|
* notice, this list of conditions and the following disclaimer.
|
|
* * Redistributions in binary form must reproduce the above
|
|
* copyright notice, this list of conditions and the following
|
|
* disclaimer in the documentation and/or other materials provided
|
|
* with the distribution.
|
|
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
|
|
* nor the names of its contributors may be used to endorse or promote
|
|
* products derived from this software without specific prior written permission.
|
|
*
|
|
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
|
|
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
|
|
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
|
|
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
|
|
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
|
|
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
|
|
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
|
|
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
|
|
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
|
|
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
|
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
|
*/
|
|
|
|
%typemap(javaimports) RDKit::RWMol "
|
|
/**
|
|
RWMol is a molecule class that is intended to be edited.
|
|
<p>
|
|
See documentation for ROMol for general remarks */"
|
|
|
|
%javamethodmodifiers RDKit::RWMol::addAtom ( ATOM_SPTR atom, bool updateLabel = true ) "
|
|
/**
|
|
<p>
|
|
adds an Atom to our collection
|
|
<p>
|
|
<p>
|
|
@param
|
|
atom pointer to the Atom to add
|
|
updateLabel (optional) if this is true, the new Atom will be our activeAtom
|
|
<p>
|
|
@return
|
|
the new number of atoms
|
|
<p>
|
|
@notes
|
|
Reimplemented from RDKit::ROMol.
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::addAtom ( Atom * atom, bool updateLabel = true, bool takeOwnership = false ) "
|
|
/**
|
|
<p>
|
|
adds an Atom to our collection
|
|
<p>
|
|
<p>
|
|
@param
|
|
atom pointer to the Atom to add
|
|
updateLabel (optional) if this is true, the new Atom will be our activeAtom
|
|
takeOwnership (optional) if this is true, we take ownership of atom instead of copying it.
|
|
<p>
|
|
@return
|
|
the new number of atoms
|
|
Reimplemented from RDKit::ROMol.
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::addAtom ( bool updateLabel = true ) "
|
|
/**
|
|
<p>
|
|
adds an empty Atom to our collection
|
|
<p>
|
|
<p>
|
|
@param
|
|
updateLabel (optional) if this is true, the new Atom will be our activeAtom
|
|
<p>
|
|
@return
|
|
the new number of atoms
|
|
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::addBond ( BOND_SPTR bsp ) "
|
|
/**
|
|
<p>
|
|
adds a Bond to our collection
|
|
<p>
|
|
<p>
|
|
@param
|
|
bond pointer to the Bond to add
|
|
<p>
|
|
@return
|
|
the new number of bonds
|
|
<p>
|
|
@notes
|
|
Reimplemented from RDKit::ROMol.
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::addBond ( Bond * bond, bool takeOwnership = false ) "
|
|
/**
|
|
<p>
|
|
adds a Bond to our collection
|
|
<p>
|
|
<p>
|
|
@param
|
|
bond pointer to the Bond to add
|
|
takeOwnership (optional) if this is true, we take ownership of bond instead of copying it.
|
|
<p>
|
|
@return
|
|
the new number of bonds
|
|
Reimplemented from RDKit::ROMol.
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::addBond ( Atom * beginAtom, Atom * endAtom, Bond::BondType order = Bond::UNSPECIFIED ) "
|
|
/**
|
|
<p>
|
|
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::addBond ( Atom::ATOM_SPTR atom1, Atom::ATOM_SPTR atom2, Bond::BondType order = Bond::UNSPECIFIED ) "
|
|
/**
|
|
<p>
|
|
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::addBond ( unsigned int beginAtomIdx, unsigned int endAtomIdx, Bond::BondType order = Bond::UNSPECIFIED ) "
|
|
/**
|
|
<p>
|
|
adds a Bond between the indicated Atoms
|
|
<p>
|
|
<p>
|
|
@return
|
|
the number of Bonds
|
|
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::createPartialBond ( unsigned int beginAtomIdx, Bond::BondType order = Bond::UNSPECIFIED ) "
|
|
/**
|
|
<p>
|
|
starts a Bond and sets its beginAtomIdx
|
|
<p>
|
|
<p>
|
|
@return
|
|
a pointer to the new bond
|
|
The caller should set a bookmark to the returned Bond in order to be able to later complete it:
|
|
<p>
|
|
Bond *pBond = mol->createPartialBond(1);
|
|
mol->setBondBookmark(pBond,666);
|
|
... do some other stuff ...
|
|
mol->finishPartialBond(2,666,Bond::SINGLE);
|
|
mol->clearBondBookmark(666,pBond);
|
|
|
|
<p>
|
|
or, if we want to set the BondType initially:
|
|
<p>
|
|
Bond *pBond = mol->createPartialBond(1,Bond::DOUBLE);
|
|
mol->setBondBookmark(pBond,666);
|
|
... do some other stuff ...
|
|
mol->finishPartialBond(2,666);
|
|
mol->clearBondBookmark(666,pBond);
|
|
|
|
<p>
|
|
the call to finishPartialBond() will take priority if you set the BondType in both calls.
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::finishPartialBond ( unsigned int endAtomIdx, int bondBookmark, Bond::BondType order = Bond::UNSPECIFIED ) "
|
|
/**
|
|
<p>
|
|
finishes a partially constructed bond
|
|
<p>
|
|
<p>
|
|
@return
|
|
the final number of Bonds
|
|
See the documentation for createPartialBond() for more details
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::getActiveAtom ( ) "
|
|
/**
|
|
<p>
|
|
<p>
|
|
@return
|
|
a pointer to the 'active' Atom
|
|
If we have an activeAtom, it will be returned, otherwise the results of getLastAtom() will be returned.
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::removeAtom ( Atom * atom ) "
|
|
/**
|
|
<p>
|
|
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::replaceAtom ( unsigned int idx, Atom * atom, bool updateLabel = false ) "
|
|
/**
|
|
<p>
|
|
replaces a particular Atom
|
|
<p>
|
|
<p>
|
|
@param
|
|
idx the index of the Atom to replace
|
|
atom the new atom, which will be copied.
|
|
updateLabel (optional) if this is true, the new Atom will be our activeAtom
|
|
|
|
*/
|
|
public";
|
|
|
|
%javamethodmodifiers RDKit::RWMol::setActiveAtom ( unsigned int idx ) "
|
|
/**
|
|
<p>
|
|
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
|
|
<p>
|
|
|
|
*/
|
|
public";
|
|
|